CurlySMILES: state and shape annotation

SSAM

A state and shape annotation is indicated by a two-character annotation marker. Letters of a state and shape annotation marker (SSAM) are in lowercase. In the following, SSAMs are listed alphabetically along with their meaning.

al atomic layer

am amorphous state

an antimatter (see examples)

aq in aqueous solution

at single atom

ay alloy

az azeotrope or component of azeotrope

br branch or branch-like structuce (mesoscale)

cl cluster (small nanoparticle containing fewer than 10⁴ atoms or molecules)

co core (in core-shell composite)

cp colloidal particle

cr crystalline state

db distributed

dp dispersed

ds dissolved (if in water, aq is preferred)

el chemical element, generic; anchored to sole square-bracket-enclosed element symbol

fw framework structure (at supramolecular level)

gr grain

gs gaseous state

ic intercalated

in incorporated (in matrix)

ip ion pair

lc liquid crystalline state

lq liquid state

ma matrix

mc micelle

ml material

mp mesoporous material

mx mixture

nb nanobelt

nc nanocrystal

nd nanodisc

nf nanoflower

nh nanowhisker

nk nanoflake

nl nanocluster

nm nanoframe

no nanoporous material

np nanoparticle, generic

nr nanorod

ns nanostructure, generic

nt nanotube

nw nanowire

pa particle

pc poly-crystalline state

po porous material

qc quasicrystalline state

qd quantum dot

s2 salt that contains two different cations or anions (double salt)

sc single-crystalline (monocrystalline) solid

sd solid state

sh shell (in core-shell composite)

su substance

tf thin film

tw twinned crystal

Examples

In a notation of a multi-species material, such as a salt in solution, the SSAM is only attached once—preferably to the right-most species. For example, the system “sodium chloride in aqueous solution” is encoded with aq anchored to the chloride ion subnotation:

[Na+].[Cl-]{aq}

“NaCl dissolved in aqueous methanol” is encoded as

[Na+].[Cl-]{dsslv=O,CO}

where the dictionary entry with key slv specifies the two solvents—comma-separated—in SMILES notation: O for water and CO for methanol.

Introductory reading

[1] Drefahl, A. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. J. Cheminf. 2011, 3:1.
DOI: 10.1186/1758-2946-3-1.

[2] Weininger, D. SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules Chem. Inf. Comput. Sci 1988, 28, pp. 31-36. DOI: 10.1021/ci00057a005.

[3] SMILES - A Simplified Chemical Language. DAYLIGHT Chemical Information Systems, Inc. URL: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html.